The correct answer is "don't worry about it" and continue on. Near the end of Deductions and Credits TT notices the orphaned 1099-DIVs and asks some questions, then adds those values to the existing form 1116. Now all 1099-DIVs are accounted for and the error flags has gone away and there is only one form 1116, unlike my 2018 return.
It seems odd to me that part of the work is done after importing the data and part is done much later in the interview. Feedback from the error flags stating that the issue will be resolved in Deductions and Credit section would be very helpful.
